Supplementary Information for sample sources: Global analysis of cytosine and adenine DNA modifications across the tree of life
All the tissues, cell lines, yeast, and bacteria samples, unless differently stated, were extracted using Genomic Tip-20 kit (Qiagen) following the manufacturer's instructions. References 1. Allen, G. C., M. A. Flores-Vergara, S. Krasynanski, S. Kumar, and W. F. Thompson. 2006. “A Modified Protocol for Rapid DNA Isolation from Plant Tissues Using Cetyltrimethylammonium Bromide.” Nature Protocols 1 (5): 2320–25. 2. Gossmann, Toni I., Achchuthan Shanmugasundram, Stefan Börno, Ludovic Duvaux, Christophe Lemaire, Heiner Kuhl, Sven Klages, et al. 2019. “Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.” Current Biology: CB 29 (10): 1712–20.e7.
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DNA extracts were treated with RNase A (VWR, Cat.No. E866-5ML) at 37 °C for 45 min and DNA purification was performed according to the manufacturer’s instructions. Purified DNA was precipitated with isopropanol, washed with 70% ethanol, and resuspended in 10 mM Tris-HCl, pH 8.0. Quantification was done using a dsDNA BR Assay Kit (Qubit). The DNA sample was then digested into corresponding nucleosides using DNA Degradase Plus (Zymo Research, E2020). One µg of DNA was treated with 5 U of DNA Degradase at 37 °C for 2 h in a final volume of 25 μl and the reaction was inactivated, incubating the samples for 20 min at 70 °C as described by the manufacturer.